FMO DATABASE

FMODB ID: ZV6GN

Calculation Name: 2VSW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VSW

Chain ID: A

ChEMBL ID:

UniProt ID: Q9BY84

Base Structure: X-ray

Registration Date: 2023-09-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	134
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1202493.681875
FMO2-HF: Nuclear repulsion	1149520.719
FMO2-HF: Total energy	-52972.962875
FMO2-MP2: Total energy	-53124.859975

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:5:MET)

Summations of interaction energy for fragment #1(A:5:MET)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-20.89	-9.961	7.015	-4.872	-13.071	-0.04

Interaction energy analysis for fragmet #1(A:5:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.079 / q_NPA : -0.029

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	7	GLY	0	0.020	0.002	3.218	0.437	3.755	1.476	-1.948	-2.846	-0.001
4	A	8	THR	0	-0.035	-0.052	3.728	0.185	-1.065	0.124	1.457	-0.332	0.000
5	A	9	GLN	0	0.054	0.013	7.415	0.336	0.336	0.000	0.000	0.000	0.000
6	A	10	ILE	0	-0.016	0.007	10.190	-0.080	-0.080	0.000	0.000	0.000	0.000
7	A	11	VAL	0	0.045	0.019	13.667	0.024	0.024	0.000	0.000	0.000	0.000
8	A	12	THR	0	0.070	0.025	16.628	-0.001	-0.001	0.000	0.000	0.000	0.000
9	A	13	GLU	-1	-0.890	-0.951	19.251	-0.072	-0.072	0.000	0.000	0.000	0.000
10	A	14	ARG	1	0.898	0.944	17.950	0.108	0.108	0.000	0.000	0.000	0.000
11	A	15	LEU	0	0.030	0.025	16.425	-0.005	-0.005	0.000	0.000	0.000	0.000
12	A	16	VAL	0	0.047	0.018	18.630	0.003	0.003	0.000	0.000	0.000	0.000
13	A	17	ALA	0	-0.018	-0.004	21.736	0.002	0.002	0.000	0.000	0.000	0.000
14	A	18	LEU	0	-0.070	-0.029	16.545	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	19	LEU	0	-0.029	-0.030	20.242	0.003	0.003	0.000	0.000	0.000	0.000
16	A	20	GLU	-1	-0.943	-0.970	22.338	-0.039	-0.039	0.000	0.000	0.000	0.000
17	A	21	SER	0	-0.074	0.002	23.032	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	22	GLY	0	0.000	-0.005	24.425	0.002	0.002	0.000	0.000	0.000	0.000
19	A	23	THR	0	-0.071	-0.048	22.187	0.004	0.004	0.000	0.000	0.000	0.000
20	A	24	GLU	-1	-0.888	-0.962	18.704	-0.123	-0.123	0.000	0.000	0.000	0.000
21	A	25	LYS	1	0.927	0.997	19.468	0.010	0.010	0.000	0.000	0.000	0.000
22	A	26	VAL	0	0.026	-0.001	16.059	-0.008	-0.008	0.000	0.000	0.000	0.000
23	A	27	LEU	0	-0.040	-0.017	13.767	0.018	0.018	0.000	0.000	0.000	0.000
24	A	28	LEU	0	0.040	0.019	14.610	-0.008	-0.008	0.000	0.000	0.000	0.000
25	A	29	ILE	0	-0.009	-0.007	11.581	0.015	0.015	0.000	0.000	0.000	0.000
26	A	30	ASP	-1	-0.731	-0.841	13.490	0.024	0.024	0.000	0.000	0.000	0.000
27	A	31	SER	0	-0.045	-0.036	11.109	0.008	0.008	0.000	0.000	0.000	0.000
28	A	32	ARG	1	0.807	0.879	13.017	-0.016	-0.016	0.000	0.000	0.000	0.000
29	A	33	PRO	0	-0.017	-0.012	15.684	0.011	0.011	0.000	0.000	0.000	0.000
30	A	34	PHE	0	0.025	-0.008	18.641	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	35	VAL	0	0.013	0.023	21.356	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	36	GLU	-1	-0.835	-0.918	19.049	0.012	0.012	0.000	0.000	0.000	0.000
33	A	37	TYR	0	-0.020	-0.006	19.583	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	38	ASN	0	-0.058	-0.033	21.370	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	39	THR	0	-0.051	-0.014	24.688	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	40	SER	0	-0.019	-0.022	24.017	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	41	HIS	1	0.817	0.914	20.397	-0.018	-0.018	0.000	0.000	0.000	0.000
38	A	42	ILE	0	0.034	0.036	17.788	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	43	LEU	0	0.029	0.014	21.482	0.005	0.005	0.000	0.000	0.000	0.000
40	A	44	GLU	-1	-0.949	-0.977	22.324	0.002	0.002	0.000	0.000	0.000	0.000
41	A	45	ALA	0	-0.034	0.010	18.049	0.001	0.001	0.000	0.000	0.000	0.000
42	A	46	ILE	0	-0.059	-0.044	17.132	0.005	0.005	0.000	0.000	0.000	0.000
43	A	47	ASN	0	-0.017	-0.005	16.721	0.002	0.002	0.000	0.000	0.000	0.000
44	A	48	ILE	0	0.006	-0.001	12.540	0.015	0.015	0.000	0.000	0.000	0.000
45	A	49	ASN	0	0.005	-0.004	14.518	-0.013	-0.013	0.000	0.000	0.000	0.000
46	A	50	CYS	0	0.042	0.030	13.144	0.020	0.020	0.000	0.000	0.000	0.000
47	A	51	SER	0	-0.056	-0.024	14.341	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	52	LYN	0	0.099	0.038	12.892	0.031	0.031	0.000	0.000	0.000	0.000
49	A	53	LEU	0	0.019	0.003	15.748	0.030	0.030	0.000	0.000	0.000	0.000
50	A	54	MET	0	0.013	0.004	14.290	0.036	0.036	0.000	0.000	0.000	0.000
51	A	55	LYS	1	0.892	0.957	9.992	-0.161	-0.161	0.000	0.000	0.000	0.000
52	A	56	ARG	1	0.954	0.992	12.330	-0.199	-0.199	0.000	0.000	0.000	0.000
53	A	57	ARG	1	0.955	0.959	14.881	-0.184	-0.184	0.000	0.000	0.000	0.000
54	A	58	LEU	0	0.033	0.027	10.408	0.023	0.023	0.000	0.000	0.000	0.000
55	A	59	GLN	0	-0.020	-0.004	10.081	0.015	0.015	0.000	0.000	0.000	0.000
56	A	60	GLN	0	-0.077	-0.033	11.357	0.039	0.039	0.000	0.000	0.000	0.000
57	A	61	ASP	-1	-0.839	-0.900	11.474	1.019	1.019	0.000	0.000	0.000	0.000
58	A	62	LYS	1	0.862	0.921	14.036	-0.424	-0.424	0.000	0.000	0.000	0.000
59	A	63	VAL	0	-0.011	-0.002	15.539	-0.055	-0.055	0.000	0.000	0.000	0.000
60	A	64	LEU	0	0.046	0.033	13.754	0.085	0.085	0.000	0.000	0.000	0.000
61	A	65	ILE	0	0.035	0.015	9.722	-0.056	-0.056	0.000	0.000	0.000	0.000
62	A	66	THR	0	0.050	0.013	12.517	-0.046	-0.046	0.000	0.000	0.000	0.000
63	A	67	GLU	-1	-0.912	-0.955	15.173	0.216	0.216	0.000	0.000	0.000	0.000
64	A	68	LEU	0	-0.006	-0.021	13.412	-0.025	-0.025	0.000	0.000	0.000	0.000
65	A	69	ILE	0	0.018	0.018	12.639	-0.028	-0.028	0.000	0.000	0.000	0.000
66	A	70	GLN	0	0.003	-0.037	16.475	-0.029	-0.029	0.000	0.000	0.000	0.000
67	A	71	HIS	0	-0.074	-0.023	19.682	-0.012	-0.012	0.000	0.000	0.000	0.000
68	A	72	SER	0	-0.043	-0.027	18.049	-0.008	-0.008	0.000	0.000	0.000	0.000
69	A	73	ALA	0	-0.048	-0.002	20.311	-0.013	-0.013	0.000	0.000	0.000	0.000
70	A	74	LYS	1	0.883	0.942	22.080	-0.062	-0.062	0.000	0.000	0.000	0.000
71	A	75	HIS	0	0.063	0.031	21.604	0.003	0.003	0.000	0.000	0.000	0.000
72	A	76	LYS	1	0.978	0.983	24.623	-0.057	-0.057	0.000	0.000	0.000	0.000
73	A	77	VAL	0	-0.024	0.007	18.709	-0.007	-0.007	0.000	0.000	0.000	0.000
74	A	78	ASP	-1	-0.870	-0.925	21.217	0.043	0.043	0.000	0.000	0.000	0.000
75	A	79	ILE	0	-0.082	-0.016	17.275	0.002	0.002	0.000	0.000	0.000	0.000
76	A	80	ASP	-1	-0.739	-0.881	17.096	0.013	0.013	0.000	0.000	0.000	0.000
77	A	81	CYS	0	-0.042	-0.017	13.536	-0.024	-0.024	0.000	0.000	0.000	0.000
78	A	82	SER	0	-0.038	-0.034	13.994	-0.050	-0.050	0.000	0.000	0.000	0.000
79	A	83	GLN	0	-0.052	-0.048	15.635	-0.024	-0.024	0.000	0.000	0.000	0.000
80	A	84	LYS	1	0.902	0.965	13.333	0.167	0.167	0.000	0.000	0.000	0.000
81	A	85	VAL	0	0.018	0.015	10.349	0.037	0.037	0.000	0.000	0.000	0.000
82	A	86	VAL	0	-0.009	0.003	10.675	-0.035	-0.035	0.000	0.000	0.000	0.000
83	A	87	VAL	0	-0.014	-0.010	8.380	0.013	0.013	0.000	0.000	0.000	0.000
84	A	88	TYR	0	0.006	-0.021	10.900	0.008	0.008	0.000	0.000	0.000	0.000
85	A	89	ASP	-1	-0.764	-0.830	11.115	-0.017	-0.017	0.000	0.000	0.000	0.000
86	A	90	GLN	0	0.082	0.023	12.945	0.002	0.002	0.000	0.000	0.000	0.000
87	A	91	SER	0	-0.046	-0.035	14.298	0.001	0.001	0.000	0.000	0.000	0.000
88	A	92	SER	0	-0.037	-0.051	9.496	-0.023	-0.023	0.000	0.000	0.000	0.000
89	A	93	GLN	0	-0.003	0.000	11.640	0.017	0.017	0.000	0.000	0.000	0.000
90	A	94	ASP	-1	-0.890	-0.953	9.072	-0.132	-0.132	0.000	0.000	0.000	0.000
91	A	95	VAL	0	0.034	0.009	2.823	-0.877	-0.431	1.501	-0.431	-1.516	0.002
92	A	96	ALA	0	-0.031	-0.003	4.830	-0.484	-0.443	-0.001	-0.003	-0.038	0.000
93	A	97	SER	0	-0.088	-0.033	6.826	-0.043	-0.043	0.000	0.000	0.000	0.000
94	A	98	LEU	0	-0.002	0.010	4.306	-0.020	0.081	-0.001	-0.005	-0.094	0.000
95	A	99	SER	0	0.004	-0.004	6.714	-0.051	-0.051	0.000	0.000	0.000	0.000
96	A	100	SER	0	0.063	0.002	5.531	-0.070	-0.070	0.000	0.000	0.000	0.000
97	A	101	ASP	-1	-0.912	-0.945	5.968	0.481	0.481	0.000	0.000	0.000	0.000
98	A	102	CYS	0	-0.077	-0.008	6.725	0.092	0.092	0.000	0.000	0.000	0.000
99	A	103	PHE	0	0.047	-0.007	7.279	0.037	0.037	0.000	0.000	0.000	0.000
100	A	104	LEU	0	0.081	0.047	5.945	0.037	0.037	0.000	0.000	0.000	0.000
101	A	105	THR	0	0.065	0.016	2.606	-0.989	-0.366	0.774	-0.258	-1.140	0.000
102	A	106	VAL	0	-0.036	-0.019	2.981	-1.267	-0.292	0.231	-0.484	-0.721	-0.006
103	A	107	LEU	0	-0.067	-0.038	5.756	0.286	0.286	0.000	0.000	0.000	0.000
104	A	108	LEU	0	0.066	0.021	2.472	-1.487	-0.092	0.703	-0.403	-1.695	-0.001
105	A	109	GLY	0	0.033	0.032	2.522	-1.833	-0.424	1.118	-0.877	-1.649	-0.002
106	A	110	LYS	1	0.776	0.871	3.215	-0.614	-1.089	0.048	0.800	-0.372	0.000
107	A	111	LEU	0	0.014	0.006	6.080	-0.029	-0.029	0.000	0.000	0.000	0.000
108	A	112	GLU	-1	-0.744	-0.885	2.789	-11.198	-6.852	1.042	-2.720	-2.668	-0.032
109	A	113	LYS	1	0.881	0.953	5.557	-3.492	-3.492	0.000	0.000	0.000	0.000
110	A	114	SER	0	-0.057	-0.023	7.348	-0.124	-0.124	0.000	0.000	0.000	0.000
111	A	115	PHE	0	-0.050	-0.024	9.274	-0.019	-0.019	0.000	0.000	0.000	0.000
112	A	116	ASN	0	0.021	0.019	8.806	-0.094	-0.094	0.000	0.000	0.000	0.000
113	A	117	SER	0	-0.062	-0.034	9.470	-0.147	-0.147	0.000	0.000	0.000	0.000
114	A	118	VAL	0	0.000	0.015	5.872	0.147	0.147	0.000	0.000	0.000	0.000
115	A	119	HIS	0	0.019	0.057	6.876	-0.077	-0.077	0.000	0.000	0.000	0.000
116	A	120	LEU	0	0.002	0.009	6.669	0.033	0.033	0.000	0.000	0.000	0.000
117	A	121	LEU	0	-0.020	-0.020	9.229	-0.054	-0.054	0.000	0.000	0.000	0.000
118	A	122	ALA	0	-0.016	-0.007	12.477	0.009	0.009	0.000	0.000	0.000	0.000
119	A	123	GLY	0	0.060	0.029	13.372	-0.009	-0.009	0.000	0.000	0.000	0.000
120	A	124	GLY	0	-0.032	-0.010	14.218	0.001	0.001	0.000	0.000	0.000	0.000
121	A	125	PHE	0	0.021	-0.003	15.053	-0.005	-0.005	0.000	0.000	0.000	0.000
122	A	126	ALA	0	-0.023	0.021	18.067	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	127	GLU	-1	-0.955	-0.972	18.376	-0.057	-0.057	0.000	0.000	0.000	0.000
124	A	128	PHE	0	0.061	0.013	18.853	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	129	SER	0	-0.021	-0.047	20.685	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	130	ARG	1	0.889	0.958	21.552	0.043	0.043	0.000	0.000	0.000	0.000
127	A	131	CYS	0	-0.088	-0.037	22.896	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	132	PHE	0	0.020	0.001	23.462	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	133	PRO	0	0.076	0.028	25.569	0.003	0.003	0.000	0.000	0.000	0.000
130	A	134	GLY	0	-0.041	-0.021	27.711	0.003	0.003	0.000	0.000	0.000	0.000
131	A	135	LEU	0	-0.004	0.007	24.852	0.001	0.001	0.000	0.000	0.000	0.000
132	A	136	CYS	0	-0.061	-0.025	24.164	0.001	0.001	0.000	0.000	0.000	0.000
133	A	137	GLU	-1	-0.903	-0.955	25.028	0.010	0.010	0.000	0.000	0.000	0.000
134	A	138	GLY	0	-0.019	-0.008	25.869	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:MET)